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As we know, when we do qRT-PCR, the two most commonly used methods are absolute quantification and relative quantification, both the methods are involved in dealing with normalization of house-keeping genes or internal control genes (like GAPDH, Actin). In the microarray experiments, the similar normalization should also be adopted (I did not have any experimence with this kind of experiment). But I do know that someone obtained GEO file from NCBI, and simply did t-test analysis to find differenced expressed genes without any operation with the internal control genes. So I wander whether this is the right way, if not, what should we do with internal control genes to normalize data?

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